Bottom Line:
It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS).In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7.The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

DSU046F7: Chromosome view of significant associations, identified for Na+/K+ ratio under stress. The alongside colour-coded graphs are representing MAF, P-value and r2 of significant SNPs from the respective chromosomes.

Mentions:
So far, ∼70 salt tolerance QTLs had been located in rice using bi-parental mapping populations,60,61 but fine mapping and narrowing down reports are limited. Only, Saltol QTL region14 has been inspected widely, and three genes (SKC1, SalT and pectinesterase) are annotated and functionally characterized in this region.62,63 The Na+/K+ ratio is an important ion balancing parameter for salt tolerance in rice, and our GWA mapping results identified this important region as a dense GWAS peak covering the Saltol region, which helps control K+ homeostasis under salinity.62 Previous studies claimed that Saltol controls salinity only at seedling stage and suggested that tolerance at seedling and reproductive stages is regulated by a different set of genes and QTLs.11 However, in our study, where all the traits were measured at reproductive stage, the Saltol region was mapped with a set of highly significant SNPs on chromosome 1. In our study, the results for Na+/K+ ratio were found more important than other traits as all the significant SNPs for this trait were found in complete LD. The results of mixed model considering Na+/K+ ratio are shown in Figs 6 and 7. The significant SNPs detected on chromosome 1 on or near the Saltol region were novel in our study and were not reported earlier from the three known genes of Saltol. All the 12 SNPs were scattered between the coordinates 9.6 and 14.5 Mb, and the top one was located at 12.8 Mb. The top hit from this region was from the coordinate 1:12854366 (LOC_Os01g22900; neutral/alkaline invertase), the other one was from the coordinate 1:12831995 (LOC_Os01g22870; expressed protein). Two significant SNPs (1: 11608731 and 12054948) from this region were between the two Saltol specific genes (SKC1 and pectinesterase). The region was found with the most prominent GWAS peak in the study with very high LD (average r2 = 0.56). Its relevance for salt tolerance in seedling stage has already been explored, and it has been widely used for introgression into a wide range of recipient elite cultivars. The mapping of novel functional allelic variants detected in the genes underlying Saltol QTL in current study at reproductive stage is a significant finding, which once validated can effectively be utilized in rice breeding programs to enhance salt tolerance.Figure 6.

DSU046F7: Chromosome view of significant associations, identified for Na+/K+ ratio under stress. The alongside colour-coded graphs are representing MAF, P-value and r2 of significant SNPs from the respective chromosomes.

Mentions:
So far, ∼70 salt tolerance QTLs had been located in rice using bi-parental mapping populations,60,61 but fine mapping and narrowing down reports are limited. Only, Saltol QTL region14 has been inspected widely, and three genes (SKC1, SalT and pectinesterase) are annotated and functionally characterized in this region.62,63 The Na+/K+ ratio is an important ion balancing parameter for salt tolerance in rice, and our GWA mapping results identified this important region as a dense GWAS peak covering the Saltol region, which helps control K+ homeostasis under salinity.62 Previous studies claimed that Saltol controls salinity only at seedling stage and suggested that tolerance at seedling and reproductive stages is regulated by a different set of genes and QTLs.11 However, in our study, where all the traits were measured at reproductive stage, the Saltol region was mapped with a set of highly significant SNPs on chromosome 1. In our study, the results for Na+/K+ ratio were found more important than other traits as all the significant SNPs for this trait were found in complete LD. The results of mixed model considering Na+/K+ ratio are shown in Figs 6 and 7. The significant SNPs detected on chromosome 1 on or near the Saltol region were novel in our study and were not reported earlier from the three known genes of Saltol. All the 12 SNPs were scattered between the coordinates 9.6 and 14.5 Mb, and the top one was located at 12.8 Mb. The top hit from this region was from the coordinate 1:12854366 (LOC_Os01g22900; neutral/alkaline invertase), the other one was from the coordinate 1:12831995 (LOC_Os01g22870; expressed protein). Two significant SNPs (1: 11608731 and 12054948) from this region were between the two Saltol specific genes (SKC1 and pectinesterase). The region was found with the most prominent GWAS peak in the study with very high LD (average r2 = 0.56). Its relevance for salt tolerance in seedling stage has already been explored, and it has been widely used for introgression into a wide range of recipient elite cultivars. The mapping of novel functional allelic variants detected in the genes underlying Saltol QTL in current study at reproductive stage is a significant finding, which once validated can effectively be utilized in rice breeding programs to enhance salt tolerance.Figure 6.

Bottom Line:
It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS).In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7.The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.